Variant report

Variant	rs10878383
Chromosome Location	chr12:66524201-66524202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:175)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:175 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:66523828-66525082	GM18505	blood:	n/a	n/a
2	MAFK	chr12:66524151-66525142	HepG2	liver:	n/a	chr12:66524718-66524729
3	IRF1	chr12:66524113-66524861	K562	blood:	n/a	n/a
4	POLR2A	chr12:66523966-66525318	GM18526	blood:	n/a	n/a
5	POLR2A	chr12:66523758-66525331	GM12878	blood:	n/a	n/a
6	MAX	chr12:66524048-66524942	Hela-S3	cervix:	n/a	n/a
7	NFIC	chr12:66524147-66524781	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:66523783-66525067	Raji	blood:	n/a	n/a
9	MYC	chr12:66524024-66525587	K562	blood:	n/a	n/a
10	MTA3	chr12:66523668-66525489	GM12878	blood:	n/a	n/a
11	RFX5	chr12:66523773-66525271	Hela-S3	cervix:	n/a	n/a
12	TAF1	chr12:66524000-66524917	A549	lung:	n/a	n/a
13	GABPA	chr12:66524087-66524938	HL-60	blood:	n/a	n/a
14	REST	chr12:66524138-66524972	HL-60	blood:	n/a	chr12:66524631-66524641
15	MAX	chr12:66524087-66524875	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr12:66524111-66524885	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr12:66523869-66525164	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr12:66523982-66525010	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr12:66524127-66524990	HepG2	liver:	n/a	n/a
20	TAF1	chr12:66524095-66525056	MCF-7	breast:	n/a	n/a
21	ELF1	chr12:66524148-66524880	SK-N-SH	brain:	n/a	chr12:66524534-66524547
22	E2F6	chr12:66524058-66524988	K562	blood:	n/a	n/a
23	MAX	chr12:66524091-66524965	MCF-7	breast:	n/a	n/a
24	POLR2A	chr12:66524197-66525017	U87	brain:	n/a	n/a
25	POLR2A	chr12:66523781-66525012	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:66524135-66525510	HUVEC	blood vessel:	n/a	n/a
27	RCOR1	chr12:66523676-66525059	K562	blood:	n/a	n/a
28	POLR2A	chr12:66523654-66524916	GM12892	blood:	n/a	n/a
29	SIN3AK20	chr12:66523966-66525089	MCF-7	breast:	n/a	n/a
30	POLR2A	chr12:66523752-66525424	U87	brain:	n/a	n/a
31	POLR2A	chr12:66523972-66525006	GM12878	blood:	n/a	n/a
32	MXI1	chr12:66523620-66525402	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr12:66523641-66525025	GM12892	blood:	n/a	n/a
34	HEY1	chr12:66523737-66524924	K562	blood:	n/a	n/a
35	MXI1	chr12:66524146-66524883	HepG2	liver:	n/a	n/a
36	STAT5A	chr12:66524047-66524743	GM12878	blood:	n/a	n/a
37	HCFC1	chr12:66523520-66525391	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr12:66523633-66524960	GM12878	blood:	n/a	n/a
39	REST	chr12:66524104-66524543	PFSK-1	brain:	n/a	n/a
40	SIN3AK20	chr12:66524157-66524794	K562	blood:	n/a	n/a
41	POLR2A	chr12:66524162-66524875	A549	lung:	n/a	n/a
42	NFATC1	chr12:66523896-66525021	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:66524003-66525010	GM12878	blood:	n/a	n/a
44	GABPA	chr12:66524024-66524982	A549	lung:	n/a	n/a
45	GABPA	chr12:66524089-66524846	Hela-S3	cervix:	n/a	n/a
46	PML	chr12:66523608-66525036	GM12878	blood:	n/a	n/a
47	MAX	chr12:66524032-66524984	ECC-1	luminal epithelium:	n/a	n/a
48	RELA	chr12:66523921-66525181	GM15510	blood:	n/a	n/a
49	ZEB1	chr12:66524109-66525035	HepG2	liver:	n/a	chr12:66524480-66524487
50	POLR2A	chr12:66524161-66526647	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66523453..66525027-chr12:66562451..66564555,2	K562	blood:
2	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
3	chr1:145096186..145098889-chr12:66522673..66525529,2	MCF-7	breast:
4	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
5	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
6	chr12:66524156..66526872-chr12:66529144..66534313,4	K562	blood:
7	chr12:66523311..66525203-chr12:66696051..66697589,2	MCF-7	breast:
8	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239335	TF binding region
ENSG00000127311	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000223380	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10400539	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10506478	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735933	0.86[CHB][hapmap]
rs10878381	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878382	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878389	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878391	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176043	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176054	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176056	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176063	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176065	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176067	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176068	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176080	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11176081	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11176082	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12227630	0.85[EUR][1000 genomes]
rs12832926	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17767200	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882201	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1898304	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1921083	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141709	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178486	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2870781	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34645929	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34755483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4474482	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4575321	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56271210	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61927092	0.83[ASN][1000 genomes]
rs7295147	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302893	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305938	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966453	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7966561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979029	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979775	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10878383	TMBIM4	cis	normal skin	skin_eQTL
rs10878383	RP11-745O10.2	cis	Thyroid	GTEx
rs10878383	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10878383	TMBIM4	cis	lesional skin	skin_eQTL
rs10878383	RP11-745O10.2	cis	Whole Blood	GTEx
rs10878383	TMBIM4	cis	uninvolved skin	skin_eQTL
rs10878383	RP11-745O10.2	cis	Artery Tibial	GTEx
rs10878383	RP11-745O10.2	cis	lung	GTEx
rs10878383	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66522600-66526000	Active TSS	GM12878-XiMat	blood
2	chr12:66523000-66525200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:66523000-66525800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:66523000-66526000	Active TSS	A549	lung
5	chr12:66523000-66526400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:66523200-66525200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:66523200-66525400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:66523400-66524400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr12:66523400-66525000	Active TSS	Fetal Lung	lung
10	chr12:66523400-66525200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:66523400-66525200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:66523400-66525200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:66523400-66525200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:66523400-66525200	Active TSS	Fetal Intestine Small	intestine
15	chr12:66523400-66525200	Active TSS	NH-A	brain
16	chr12:66523400-66525200	Active TSS	NHDF-Ad	bronchial
17	chr12:66523400-66525400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:66523400-66525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:66523400-66525400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:66523400-66525400	Active TSS	HSMMtube	muscle
21	chr12:66523400-66525400	Active TSS	NHLF	lung
22	chr12:66523400-66525600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:66523400-66525800	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr12:66523600-66524400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr12:66523600-66524400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr12:66523600-66524400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:66523600-66525000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:66523600-66525000	Active TSS	Gastric	stomach
29	chr12:66523600-66525000	Active TSS	Lung	lung
30	chr12:66523600-66525200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr12:66523600-66525200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:66523600-66525200	Active TSS	H9 Cell Line	embryonic stem cell
33	chr12:66523600-66525200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr12:66523600-66525400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:66523600-66525400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:66523600-66525400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:66523600-66525400	Active TSS	Fetal Muscle Trunk	muscle
38	chr12:66523600-66525400	Active TSS	Left Ventricle	heart
39	chr12:66523600-66525400	Active TSS	Ovary	ovary
40	chr12:66523600-66525400	Active TSS	Psoas Muscle	Psoas
41	chr12:66523600-66525400	Active TSS	Right Atrium	heart
42	chr12:66523600-66525600	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr12:66523800-66524800	Active TSS	Rectal Smooth Muscle	rectum
44	chr12:66523800-66524800	Active TSS	HUVEC	blood vessel
45	chr12:66523800-66525000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:66523800-66525000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:66523800-66525000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:66523800-66525000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:66523800-66525000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:66523800-66525000	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links